I keep a cheque register; it just basic. I list ALL the cheques I receive on there; Date, name, address, amount - I don't think there's a need to write sort codes or account numbers.
Then when I pay them into the bank, total the list up, write the figure under the amount column and the date you put them in the bank.
In this way I KNOW whether I've received a cheque or not - I don't have to ask a customer to check her/his stub or statements. It safeguards against receiving a cheque, banking it, and not marking it as paid and asking for payment again.